[English] 日本語
Yorodumi- PDB-3wi6: Crystal structure of MAPKAP Kinase-2 (MK2) in complex with non-se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wi6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MAPKAP Kinase-2 (MK2) in complex with non-selective inhibitor | ||||||
Components | MAP kinase-activated protein kinase 2 | ||||||
Keywords | Transferase/Transferase inhibitor / Gly-rich loop formed / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase-Transferase inhibitor complex | ||||||
Function / homology | Function and homology information macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production ...macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / calcium-dependent protein serine/threonine kinase activity / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / calcium/calmodulin-dependent protein kinase activity / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / non-specific serine/threonine protein kinase / calmodulin binding / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Fujino, A. / Fukushima, K. / Kubota, T. / Matsumoto, Y. / Takimoto-Kamimura, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of the beta-form of human MK2 in complex with the non-selective kinase inhibitor TEI-L03090 Authors: Fujino, A. / Fukushima, K. / Kubota, T. / Matsumoto, Y. / Takimoto-Kamimura, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wi6.cif.gz | 339.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wi6.ent.gz | 276.2 KB | Display | PDB format |
PDBx/mmJSON format | 3wi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wi6_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wi6_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3wi6_validation.xml.gz | 60.4 KB | Display | |
Data in CIF | 3wi6_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wi6 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wi6 | HTTPS FTP |
-Related structure data
Related structure data | 1ny3S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37521.332 Da / Num. of mol.: 6 / Fragment: UNP residues 41-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P49137, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-YRZ / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Na-Acetate, 1.6M Ammonium Sulphate, 200mM NaCl, 1.4mM Deoxi Big Chap, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→100 Å / Num. obs: 82725 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NY3 Resolution: 2.99→30 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.826 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.368 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.988→3.065 Å / Total num. of bins used: 20
|